Starting phenix.real_space_refine
on Tue Feb 13 14:19:36 2024 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlq_27510/02_2024/8dlq_27510.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlq_27510/02_2024/8dlq_27510.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlq_27510/02_2024/8dlq_27510.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlq_27510/02_2024/8dlq_27510.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlq_27510/02_2024/8dlq_27510.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlq_27510/02_2024/8dlq_27510.pdb"
  }
  resolution = 2.77
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.035
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    4190      2.51       5
     N    1077      2.21       5
     O    1248      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "B TYR  351": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE  327": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 6552
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1592
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1592
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 11, 'TRANS': 189}
    Chain: "E"
      Number of atoms: 4862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 27, 'TRANS': 568}
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 3.94, per 1000 atoms: 0.60
  Number of scatterers: 6552
  At special positions: 0
  Unit cell: (80, 83, 122, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    1248      8.00
     N    1077      7.00
     C    4190      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 133 " - pdb=" SG  CYS E 141 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 530 " - pdb=" SG  CYS E 542 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG B1301 " - " ASN B 343 "
      " NAG E 701 " - " ASN E  53 "
      " NAG E 702 " - " ASN E  90 "
      " NAG E 703 " - " ASN E 103 "
      " NAG E 704 " - " ASN E 322 "
      " NAG E 705 " - " ASN E 432 "
      " NAG E 706 " - " ASN E 546 "
  Time building additional restraints: 2.32
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1500

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 7 sheets defined
      57.8% alpha, 6.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.74
  Creating SS restraints...
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 365 through 370
    Processing helix  chain 'B' and resid 383 through 387
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 4.013A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.568A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 20 through 53
      removed outlier: 3.645A  pdb=" N   ASP E  38 " --> pdb=" O   HIS E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 81
    Processing helix  chain 'E' and resid 82 through 83
      No H-bonds generated for 'chain 'E' and resid 82 through 83'
    Processing helix  chain 'E' and resid 84 through 88
      removed outlier: 3.692A  pdb=" N   GLU E  87 " --> pdb=" O   PRO E  84 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 90 through 101
    Processing helix  chain 'E' and resid 103 through 108
      removed outlier: 4.030A  pdb=" N   VAL E 107 " --> pdb=" O   GLY E 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 109 through 129
    Processing helix  chain 'E' and resid 147 through 155
    Processing helix  chain 'E' and resid 157 through 194
      Proline residue:  E 178  - end of helix
      removed outlier: 3.693A  pdb=" N   VAL E 185 " --> pdb=" O   GLU E 181 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 198 through 205
    Processing helix  chain 'E' and resid 206 through 208
      No H-bonds generated for 'chain 'E' and resid 206 through 208'
    Processing helix  chain 'E' and resid 218 through 252
      removed outlier: 3.742A  pdb=" N   LEU E 222 " --> pdb=" O   SER E 218 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   ILE E 223 " --> pdb=" O   ARG E 219 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   GLU E 224 " --> pdb=" O   GLY E 220 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   GLU E 232 " --> pdb=" O   HIS E 228 " (cutoff:3.500A)
      Proline residue:  E 235  - end of helix
    Processing helix  chain 'E' and resid 265 through 267
      No H-bonds generated for 'chain 'E' and resid 265 through 267'
    Processing helix  chain 'E' and resid 275 through 279
      removed outlier: 3.793A  pdb=" N   TYR E 279 " --> pdb=" O   THR E 276 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 293 through 300
    Processing helix  chain 'E' and resid 303 through 318
    Processing helix  chain 'E' and resid 324 through 331
    Processing helix  chain 'E' and resid 365 through 385
    Processing helix  chain 'E' and resid 386 through 388
      No H-bonds generated for 'chain 'E' and resid 386 through 388'
    Processing helix  chain 'E' and resid 389 through 393
    Processing helix  chain 'E' and resid 397 through 413
      removed outlier: 4.296A  pdb=" N   HIS E 401 " --> pdb=" O   ASN E 397 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   GLU E 402 " --> pdb=" O   GLU E 398 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   GLY E 405 " --> pdb=" O   HIS E 401 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   MET E 408 " --> pdb=" O   VAL E 404 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 414 through 421
    Processing helix  chain 'E' and resid 431 through 447
      removed outlier: 3.509A  pdb=" N   GLU E 435 " --> pdb=" O   ASP E 431 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 448 through 465
      removed outlier: 4.315A  pdb=" N   PHE E 452 " --> pdb=" O   GLY E 448 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 469 through 471
      No H-bonds generated for 'chain 'E' and resid 469 through 471'
    Processing helix  chain 'E' and resid 472 through 484
    Processing helix  chain 'E' and resid 499 through 502
      removed outlier: 3.654A  pdb=" N   SER E 502 " --> pdb=" O   ASP E 499 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 499 through 502'
    Processing helix  chain 'E' and resid 503 through 508
    Processing helix  chain 'E' and resid 512 through 533
      removed outlier: 4.420A  pdb=" N   TYR E 516 " --> pdb=" O   PHE E 512 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   PHE E 523 " --> pdb=" O   THR E 519 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 538 through 542
    Processing helix  chain 'E' and resid 547 through 559
      removed outlier: 3.851A  pdb=" N   MET E 557 " --> pdb=" O   LYS E 553 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 565 through 574
    Processing helix  chain 'E' and resid 581 through 588
    Processing helix  chain 'E' and resid 588 through 599
    Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.864A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   GLU B 516 " --> pdb=" O   ASN B 394 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392
    Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'E' and resid 131 through 132
      removed outlier: 3.578A  pdb=" N   LEU E 142 " --> pdb=" O   VAL E 132 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 262 through 263
      removed outlier: 6.123A  pdb=" N   LEU E 262 " --> pdb=" O   VAL E 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 347 through 352
      removed outlier: 6.521A  pdb=" N   ASP E 355 " --> pdb=" O   LEU E 351 " (cutoff:3.500A)

    326 hydrogen bonds defined for protein.
    924 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.80

  Time building geometry restraints manager: 2.53 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.35: 2079
        1.35 -     1.47: 1810
        1.47 -     1.60: 2788
        1.60 -     1.72: 0
        1.72 -     1.85: 58
  Bond restraints: 6735
  Sorted by residual:
  bond pdb=" C1  NAG E 701 "
       pdb=" O5  NAG E 701 "
    ideal  model  delta    sigma   weight residual
    1.406  1.489 -0.083 2.00e-02 2.50e+03 1.72e+01
  bond pdb=" C1  NAG E 703 "
       pdb=" O5  NAG E 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.459 -0.053 2.00e-02 2.50e+03 6.95e+00
  bond pdb=" C1  NAG E 702 "
       pdb=" O5  NAG E 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.457 -0.051 2.00e-02 2.50e+03 6.52e+00
  bond pdb=" C1  NAG E 704 "
       pdb=" O5  NAG E 704 "
    ideal  model  delta    sigma   weight residual
    1.406  1.453 -0.047 2.00e-02 2.50e+03 5.58e+00
  bond pdb=" C   GLU E 145 "
       pdb=" N   PRO E 146 "
    ideal  model  delta    sigma   weight residual
    1.334  1.388 -0.054 2.34e-02 1.83e+03 5.31e+00
  ... (remaining 6730 not shown)

  Histogram of bond angle deviations from ideal:
       97.48 -   104.81: 147
      104.81 -   112.14: 3118
      112.14 -   119.48: 2383
      119.48 -   126.81: 3378
      126.81 -   134.14: 128
  Bond angle restraints: 9154
  Sorted by residual:
  angle pdb=" CA  TYR B 495 "
        pdb=" CB  TYR B 495 "
        pdb=" CG  TYR B 495 "
      ideal   model   delta    sigma   weight residual
     113.90  122.91   -9.01 1.80e+00 3.09e-01 2.51e+01
  angle pdb=" CA  TYR E 385 "
        pdb=" CB  TYR E 385 "
        pdb=" CG  TYR E 385 "
      ideal   model   delta    sigma   weight residual
     113.90  122.12   -8.22 1.80e+00 3.09e-01 2.08e+01
  angle pdb=" C   SER B 359 "
        pdb=" N   ASN B 360 "
        pdb=" CA  ASN B 360 "
      ideal   model   delta    sigma   weight residual
     122.36  128.19   -5.83 1.42e+00 4.96e-01 1.69e+01
  angle pdb=" CA  ASN E 437 "
        pdb=" CB  ASN E 437 "
        pdb=" CG  ASN E 437 "
      ideal   model   delta    sigma   weight residual
     112.60  116.03   -3.43 1.00e+00 1.00e+00 1.18e+01
  angle pdb=" CA  ASN B 360 "
        pdb=" CB  ASN B 360 "
        pdb=" CG  ASN B 360 "
      ideal   model   delta    sigma   weight residual
     112.60  115.96   -3.36 1.00e+00 1.00e+00 1.13e+01
  ... (remaining 9149 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.95: 3690
       16.95 -    33.90: 309
       33.90 -    50.85: 38
       50.85 -    67.80: 17
       67.80 -    84.75: 10
  Dihedral angle restraints: 4064
    sinusoidal: 1725
      harmonic: 2339
  Sorted by residual:
  dihedral pdb=" SG  CYS B 391 "
           pdb=" CB  CYS B 525 "
           pdb=" SG  CYS B 525 "
           pdb=" CA  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   15.31   63.69     1      2.00e+01 2.50e-03 1.34e+01
  dihedral pdb=" SG  CYS E 133 "
           pdb=" CB  CYS E 141 "
           pdb=" SG  CYS E 141 "
           pdb=" CA  CYS E 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   16.53   62.47     1      2.00e+01 2.50e-03 1.29e+01
  dihedral pdb=" C   ASN B 360 "
           pdb=" N   ASN B 360 "
           pdb=" CA  ASN B 360 "
           pdb=" CB  ASN B 360 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.95    8.35     0      2.50e+00 1.60e-01 1.12e+01
  ... (remaining 4061 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 687
       0.053 -    0.106: 213
       0.106 -    0.159: 63
       0.159 -    0.212: 14
       0.212 -    0.265: 2
  Chirality restraints: 979
  Sorted by residual:
  chirality pdb=" CB  VAL E 581 "
            pdb=" CA  VAL E 581 "
            pdb=" CG1 VAL E 581 "
            pdb=" CG2 VAL E 581 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" CA  ASN B 360 "
            pdb=" N   ASN B 360 "
            pdb=" C   ASN B 360 "
            pdb=" CB  ASN B 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.69e+00
  chirality pdb=" CA  ASN E 437 "
            pdb=" N   ASN E 437 "
            pdb=" C   ASN E 437 "
            pdb=" CB  ASN E 437 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.09e+00
  ... (remaining 976 not shown)

  Planarity restraints: 1183
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG E 169 "    0.014 2.00e-02 2.50e+03   2.91e-02 8.48e+00
        pdb=" C   ARG E 169 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   ARG E 169 "    0.019 2.00e-02 2.50e+03
        pdb=" N   SER E 170 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 495 "   -0.030 2.00e-02 2.50e+03   1.96e-02 7.68e+00
        pdb=" CG  TYR B 495 "    0.046 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 495 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 495 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 495 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 495 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 495 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B 495 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU E 589 "   -0.046 5.00e-02 4.00e+02   6.90e-02 7.62e+00
        pdb=" N   PRO E 590 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO E 590 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO E 590 "   -0.039 5.00e-02 4.00e+02
  ... (remaining 1180 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1891
        2.82 -     3.34: 6027
        3.34 -     3.86: 11482
        3.86 -     4.38: 13057
        4.38 -     4.90: 22523
  Nonbonded interactions: 54980
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E 183 "
            pdb=" OD1 ASP E 509 "
     model   vdw
     2.296 2.440
  nonbonded pdb=" O   MET E 152 "
            pdb=" NH1 ARG E 161 "
     model   vdw
     2.353 2.520
  nonbonded pdb=" O   ASN E 117 "
            pdb=" ND2 ASN E 121 "
     model   vdw
     2.354 2.520
  nonbonded pdb=" OH  TYR E 237 "
            pdb=" O   VAL E 485 "
     model   vdw
     2.370 2.440
  nonbonded pdb=" OD2 ASP B 398 "
            pdb=" OH  TYR B 423 "
     model   vdw
     2.384 2.440
  ... (remaining 54975 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          13.200
  Check model and map are aligned:         0.100
  Set scattering table:                    0.070
  Process input model:                     21.910
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   51.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8561
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.083   6735  Z= 0.375
  Angle     :  0.909   9.012   9154  Z= 0.520
  Chirality :  0.059   0.265    979
  Planarity :  0.007   0.069   1176
  Dihedral  : 13.162  84.755   2546
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  4.29 %
    Favored  : 95.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.27), residues: 793
  helix:  0.75 (0.24), residues: 391
  sheet:  1.02 (0.65), residues: 42
  loop : -0.35 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP E 566 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.029   0.003   PHE E 369 
 TYR   0.046   0.002   TYR B 495 
 ARG   0.010   0.001   ARG E 460 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 90
  time to evaluate  : 0.757 
Fit side-chains
REVERT: B  386 LYS cc_start: 0.8764 (pttm) cc_final: 0.8134 (pttm)
REVERT: B  390 LEU cc_start: 0.8852 (mt) cc_final: 0.8415 (mt)
REVERT: E  117 ASN cc_start: 0.8976 (t0) cc_final: 0.8351 (p0)
REVERT: E  121 ASN cc_start: 0.8679 (m-40) cc_final: 0.8439 (m110)
  outliers start: 3
  outliers final: 0
  residues processed: 93
  average time/residue: 1.3714
  time to fit residues: 133.5406
Evaluate side-chains
  56 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 40 optimal weight:    0.4980
   chunk 31 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 498 GLN
E  42 GLN
E 374 HIS
E 552 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.1994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6735  Z= 0.270
  Angle     :  0.569   9.190   9154  Z= 0.293
  Chirality :  0.042   0.131    979
  Planarity :  0.004   0.040   1176
  Dihedral  :  5.259  57.127   1013
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 10.29 %
    Favored  : 87.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.28), residues: 793
  helix:  1.45 (0.25), residues: 404
  sheet:  0.96 (0.74), residues: 42
  loop : -0.00 (0.31), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 374 
 PHE   0.019   0.002   PHE E 369 
 TYR   0.027   0.001   TYR B 495 
 ARG   0.005   0.000   ARG B 346 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 55
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
REVERT: B  457 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.8770 (mtp85)
REVERT: B  528 LYS cc_start: 0.3683 (OUTLIER) cc_final: 0.3319 (pttp)
REVERT: E  117 ASN cc_start: 0.8950 (t0) cc_final: 0.8388 (p0)
REVERT: E  121 ASN cc_start: 0.8783 (m-40) cc_final: 0.8492 (m110)
REVERT: E  541 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8607 (mmtm)
  outliers start: 13
  outliers final: 4
  residues processed: 65
  average time/residue: 1.3655
  time to fit residues: 93.4719
Evaluate side-chains
  58 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  457 ARG
Chi-restraints excluded: chain B residue  523 THR
Chi-restraints excluded: chain B residue  528 LYS
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  541 LYS
Chi-restraints excluded: chain E residue  579 MET
Chi-restraints excluded: chain E residue  613 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 59 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 57 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.8584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.2343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6735  Z= 0.231
  Angle     :  0.540   9.724   9154  Z= 0.277
  Chirality :  0.040   0.128    979
  Planarity :  0.004   0.041   1176
  Dihedral  :  5.000  57.103   1013
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  1.13 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 11.71 %
    Favored  : 86.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.29), residues: 793
  helix:  1.82 (0.26), residues: 392
  sheet:  0.80 (0.78), residues: 43
  loop :  0.17 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.018   0.001   PHE E 369 
 TYR   0.022   0.001   TYR B 495 
 ARG   0.004   0.000   ARG B 346 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 56
  time to evaluate  : 0.764 
Fit side-chains
   revert: symmetry clash
REVERT: B  458 LYS cc_start: 0.8667 (mmpt) cc_final: 0.8409 (mmtt)
REVERT: E  117 ASN cc_start: 0.8943 (t0) cc_final: 0.8337 (p0)
REVERT: E  121 ASN cc_start: 0.8788 (m-40) cc_final: 0.8494 (m110)
REVERT: E  291 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8118 (pp)
REVERT: E  480 MET cc_start: 0.9042 (mtp) cc_final: 0.8831 (mtm)
  outliers start: 16
  outliers final: 6
  residues processed: 66
  average time/residue: 1.4011
  time to fit residues: 97.2759
Evaluate side-chains
  62 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain B residue  523 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  291 ILE
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 37 optimal weight:    0.0040
   chunk 7 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0370
   chunk 63 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.4470

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
moved from start:          0.2517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6735  Z= 0.160
  Angle     :  0.488   6.393   9154  Z= 0.247
  Chirality :  0.039   0.125    979
  Planarity :  0.003   0.043   1176
  Dihedral  :  4.797  57.455   1013
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 12.86 %
    Favored  : 85.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.30), residues: 793
  helix:  1.93 (0.26), residues: 400
  sheet:  0.82 (0.78), residues: 43
  loop :  0.22 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 374 
 PHE   0.015   0.001   PHE E 369 
 TYR   0.018   0.001   TYR B 495 
 ARG   0.005   0.000   ARG B 346 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 57
  time to evaluate  : 0.738 
Fit side-chains
   revert: symmetry clash
REVERT: B  523 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8487 (t)
REVERT: E  117 ASN cc_start: 0.8942 (t0) cc_final: 0.8442 (t0)
REVERT: E  121 ASN cc_start: 0.8759 (m-40) cc_final: 0.8331 (m110)
REVERT: E  291 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8130 (pp)
REVERT: E  571 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8404 (tt0)
  outliers start: 14
  outliers final: 5
  residues processed: 65
  average time/residue: 1.3496
  time to fit residues: 92.3546
Evaluate side-chains
  60 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 52
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  523 THR
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain E residue  291 ILE
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  571 GLU
Chi-restraints excluded: chain E residue  579 MET
Chi-restraints excluded: chain E residue  613 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 31 optimal weight:   10.0000
   chunk 65 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 388 ASN
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 154 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.2742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6735  Z= 0.236
  Angle     :  0.522   6.599   9154  Z= 0.265
  Chirality :  0.040   0.127    979
  Planarity :  0.003   0.041   1176
  Dihedral  :  4.805  57.771   1013
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 13.29 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.30), residues: 793
  helix:  1.82 (0.26), residues: 412
  sheet:  0.81 (0.79), residues: 43
  loop :  0.37 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 374 
 PHE   0.017   0.001   PHE E 369 
 TYR   0.021   0.001   TYR B 495 
 ARG   0.004   0.000   ARG B 346 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 54
  time to evaluate  : 1.145 
Fit side-chains
   revert: symmetry clash
REVERT: B  518 LEU cc_start: 0.8800 (mt) cc_final: 0.8374 (tt)
REVERT: B  523 THR cc_start: 0.8770 (OUTLIER) cc_final: 0.8529 (t)
REVERT: E  117 ASN cc_start: 0.9006 (t0) cc_final: 0.8499 (t0)
REVERT: E  121 ASN cc_start: 0.8796 (m-40) cc_final: 0.8301 (m110)
  outliers start: 17
  outliers final: 4
  residues processed: 65
  average time/residue: 1.5177
  time to fit residues: 104.5934
Evaluate side-chains
  56 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  388 ASN
Chi-restraints excluded: chain B residue  523 THR
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 76 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 40 optimal weight:    0.7980
   chunk 73 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   chunk 55 optimal weight:    4.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 388 ASN
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  98 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.2842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6735  Z= 0.218
  Angle     :  0.512   6.913   9154  Z= 0.258
  Chirality :  0.040   0.127    979
  Planarity :  0.003   0.041   1176
  Dihedral  :  4.758  58.192   1013
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 13.86 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.30), residues: 793
  helix:  1.83 (0.26), residues: 412
  sheet:  0.77 (0.80), residues: 43
  loop :  0.44 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.016   0.001   PHE E 369 
 TYR   0.018   0.001   TYR B 495 
 ARG   0.006   0.000   ARG B 346 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 53
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
REVERT: B  523 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8486 (t)
  outliers start: 15
  outliers final: 8
  residues processed: 64
  average time/residue: 1.3679
  time to fit residues: 92.1253
Evaluate side-chains
  59 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  388 ASN
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain B residue  523 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  141 CYS
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 43 optimal weight:    0.2980
   chunk 64 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0270
   chunk 46 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 45 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9990
   chunk 14 optimal weight:    3.9990
   overall best weight:    0.6040

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 388 ASN
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.2910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6735  Z= 0.190
  Angle     :  0.512   7.750   9154  Z= 0.259
  Chirality :  0.040   0.127    979
  Planarity :  0.003   0.041   1176
  Dihedral  :  4.704  58.182   1013
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 14.57 %
    Favored  : 83.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.30), residues: 793
  helix:  1.93 (0.26), residues: 406
  sheet:  0.82 (0.80), residues: 43
  loop :  0.42 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.015   0.001   PHE E 369 
 TYR   0.017   0.001   TYR B 495 
 ARG   0.007   0.000   ARG B 346 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8683 (pt0) cc_final: 0.8407 (pm20)
REVERT: B  518 LEU cc_start: 0.8846 (mt) cc_final: 0.8424 (tt)
REVERT: B  523 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8466 (t)
REVERT: E  291 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8114 (pp)
  outliers start: 14
  outliers final: 6
  residues processed: 62
  average time/residue: 1.3326
  time to fit residues: 87.5685
Evaluate side-chains
  58 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  388 ASN
Chi-restraints excluded: chain B residue  523 THR
Chi-restraints excluded: chain E residue  141 CYS
Chi-restraints excluded: chain E residue  291 ILE
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 37 optimal weight:    0.2980
   chunk 7 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9990
   chunk 70 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.7384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 388 ASN
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.2938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6735  Z= 0.212
  Angle     :  0.523   7.598   9154  Z= 0.263
  Chirality :  0.040   0.127    979
  Planarity :  0.003   0.040   1176
  Dihedral  :  4.696  58.330   1013
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 15.29 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.30), residues: 793
  helix:  1.90 (0.26), residues: 412
  sheet:  0.77 (0.79), residues: 43
  loop :  0.51 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.016   0.001   PHE E 369 
 TYR   0.018   0.001   TYR B 495 
 ARG   0.007   0.000   ARG B 346 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 50
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8673 (pt0) cc_final: 0.8394 (pm20)
REVERT: B  458 LYS cc_start: 0.8748 (mmpt) cc_final: 0.8532 (mmtt)
REVERT: B  523 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8450 (t)
  outliers start: 13
  outliers final: 8
  residues processed: 59
  average time/residue: 1.2657
  time to fit residues: 79.0212
Evaluate side-chains
  59 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain B residue  523 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  141 CYS
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  579 MET
Chi-restraints excluded: chain E residue  613 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.9782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 388 ASN
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8638
moved from start:          0.2997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6735  Z= 0.253
  Angle     :  0.532   7.283   9154  Z= 0.269
  Chirality :  0.040   0.128    979
  Planarity :  0.004   0.040   1176
  Dihedral  :  4.758  58.566   1013
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 15.43 %
    Favored  : 83.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.30), residues: 793
  helix:  1.91 (0.26), residues: 406
  sheet:  0.92 (0.80), residues: 42
  loop :  0.43 (0.35), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.016   0.001   PHE E 369 
 TYR   0.018   0.001   TYR B 495 
 ARG   0.008   0.000   ARG B 346 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.807 
Fit side-chains
   revert: symmetry clash
REVERT: B  458 LYS cc_start: 0.8743 (mmpt) cc_final: 0.8491 (mmtt)
REVERT: B  523 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8455 (t)
  outliers start: 10
  outliers final: 8
  residues processed: 57
  average time/residue: 1.6940
  time to fit residues: 101.8854
Evaluate side-chains
  56 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  388 ASN
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain B residue  523 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  141 CYS
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 72 optimal weight:    0.0040
   chunk 62 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0980
   chunk 66 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 57 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.4992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 388 ASN
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
moved from start:          0.3002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6735  Z= 0.175
  Angle     :  0.521   8.328   9154  Z= 0.261
  Chirality :  0.039   0.126    979
  Planarity :  0.003   0.040   1176
  Dihedral  :  4.677  58.531   1013
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 16.14 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.30), residues: 793
  helix:  1.89 (0.26), residues: 412
  sheet:  0.70 (0.79), residues: 43
  loop :  0.49 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 374 
 PHE   0.015   0.001   PHE E 369 
 TYR   0.015   0.001   TYR B 495 
 ARG   0.009   0.000   ARG B 346 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.819 
Fit side-chains
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8642 (pt0) cc_final: 0.8384 (pm20)
REVERT: B  458 LYS cc_start: 0.8750 (mmpt) cc_final: 0.8493 (mmtt)
REVERT: B  518 LEU cc_start: 0.8880 (mt) cc_final: 0.8461 (tt)
  outliers start: 9
  outliers final: 6
  residues processed: 55
  average time/residue: 1.4131
  time to fit residues: 81.9977
Evaluate side-chains
  53 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain E residue  141 CYS
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  491 VAL
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 71 optimal weight:    0.0000
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.7186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 388 ASN
** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.066004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.049374 restraints weight = 17561.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.2793 rms_B_bonded: 3.03
r_work: 0.2650 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.3045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6735  Z= 0.208
  Angle     :  0.524   7.732   9154  Z= 0.265
  Chirality :  0.040   0.128    979
  Planarity :  0.003   0.040   1176
  Dihedral  :  4.673  58.573   1013
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 16.14 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.30), residues: 793
  helix:  1.89 (0.26), residues: 412
  sheet:  0.89 (0.79), residues: 42
  loop :  0.49 (0.35), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.016   0.001   PHE E 369 
 TYR   0.017   0.001   TYR B 495 
 ARG   0.009   0.000   ARG B 346 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2574.82 seconds
wall clock time: 46 minutes 54.75 seconds (2814.75 seconds total)